Ecological surveys are the basic tool incorporated into almost every study AP Marine carries out. A variety of methodologies are utilised on various habitats whether these are sandy and muddy bottoms, seagrass meadows or hard substrate bottoms, shallow or deep sites.

Ecological surveys consist of macrofauna surveys, algal and angiosperm surveys, surveys on ichthyofauna, as well as general descriptions of biomes ecosystems and biodiversity.  AP Marine utilises its own database of local organisms that has been developed to aid in identification and taxonomy. Scientists at AP Marine specialise in taxonomy and particularly in macrofauna identification, with a large amount of samples being processed every year. Ichthyology surveys are conducted both using sampling (fishing) techniques as well as utilising non destructive visual census methods.